I agree that the Wild Animal Park is a bit more fun than the Zoo. BUT if you're wanting to stay in the downtown area, then go for the Zoo.
I think that South Beach Bar & Grillle in Ocean Beach has the BEST fish tacos. Their address is 5059 Newport Ave in San Diego. Also in the Ocean Beach area is Hodad's. They're famous for their burgers. I haven't tried them, but people say they're the best in SD. They're located on 5010 Newport Ave.
If you're wanting a more "natural" views, I highly recommend Cabrillo National Monument. The views are phenomenal and there's a little paved trail that has great views.
If you're looking to do some shopping, the Fashion Valley Mall is the best in SD--it's got NM, Saks, Bloomies, Nordy's and a JC Penney. Then there are boutiques like LV, Burberry, Max Mara but stores like the Gap, Old Navy, Sephora.
Not so sure what to recommend for "unique" edibles... There's a dessert place called Extraordinary Desserts that a lot of people love in SD. They've got two locations. They also sell unique teas, jams, etc. You can check out there site:
http://www.extraordinarydesserts.com/extraordinarygourmet_store.htm
Since you're coming out Labor Day weekend, I'd find a place to stay ASAP. SD's a very popular destination for that weekend. If you've got any more questions, feel free to PM me or post it here!